SPIKE – a database, visualization and analysis tool of cellular signaling pathways

<p>Abstract</p> <p>Background</p> <p>Biological signaling pathways that govern cellular physiology form an intricate web of tightly regulated interlocking processes. Data on these regulatory networks are accumulating at an unprecedented pace. The assimilation, visualization and interpretation of these data have become a major challenge in biological research, and once met, will greatly boost our ability to understand cell functioning on a systems level.</p> <p>Results</p> <p>To cope with this challenge, we are developing the SPIKE knowledge-base of signaling pathways. SPIKE contains three main software components: 1) A database (DB) of biological signaling pathways. Carefully curated information from the literature and data from large public sources constitute distinct tiers of the DB. 2) A visualization package that allows interactive graphic representations of regulatory interactions stored in the DB and superposition of functional genomic and proteomic data on the maps. 3) An algorithmic inference engine that analyzes the networks for novel functional interplays between network components.</p> <p>SPIKE is designed and implemented as a community tool and therefore provides a user-friendly interface that allows registered users to upload data to SPIKE DB. Our vision is that the DB will be populated by a distributed and highly collaborative effort undertaken by multiple groups in the research community, where each group contributes data in its field of expertise.</p> <p>Conclusion</p> <p>The integrated capabilities of SPIKE make it a powerful platform for the analysis of signaling networks and the integration of knowledge on such networks with <it>omics </it>data. </p

The duality of service: between honour and humiliation, between primary and secondary functions

This chapter revisits a celebrated act of court ritual: the gesture of handing the king his chemise as he rose each morning. Re-contextualizing this gesture thematically, socially, chronologically, and functionally, I underscore the duality of such ‘honourable service’ and the degree to which it was shaped by extra-royal agendas even in the heyday of the Sun King. In place well before Louis XIV, these acts occurred in sub-royal as well as in royal settings; in the former, a more complicated perception of service emerges, of a humiliating task as well as a ‘prestige fetish’. Givers, moreover, were also receivers: each time an aristocrat was to hand the king the chemise, he would receive it from others; often, this was the more important interaction. The final section uncovers the macro-political stakes of these acts in the struggle of the Legitimated Princes to equate themselves with the legitimate princes of royal blood

The Culture of Orders : Status Interactions during the Reign of Louis XIV

EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Writing to undo: protestation as a mode of early modern resistance

This study investigates protestations as a unique lens into the workings of coercion and resistance in the early modern period. Protestation was a wide-ranging genre of document, written to counter the consequences of coercive forces in myriad forms: familial, economic, religious, and political; on the levels of micro and macro; and across social and geographical space. This remarkable scope has paradoxically proven an obstacle to realizing the historiographical potential of the phenomenon, which remains largely uncharted and familiar only to a few specialists separated by sub-disciplinary divides. This article thus offers a unifying conceptual, analytic, and methodological framework. It interrogates protestations as material objects as well as verbal texts; follows them throughout their lifecycle; and explores their spectra of producers, protagonists, and functions. A variety of case studies from the ancien régime illustrate the significance of the phenomenon on both the micro and macro levels, whether in the struggles of young people against the abuses of patriarchal and familial authority or in the subversive use of protestations in the constitutional crises of absolute monarchy. Protestation is thus shown to be of wide interest to a broad swath of scholars, including historians of gender, family, working-people, elites, high politics, law, and writing

Sulfometuron incorporation in cationic micelles adsorbed on montmorillonite

The aim of this study was to understand the interactions between alkylammonium cations present as monomers and micelles and a clay mineral, montmorillonite, to develop slow release formulations of anionic herbicides, such as sulfometuron (SFM) whose leaching in soils is an environmental and economic problem. In the proposed formulation the herbicide is incorporated in positively charged micelles of quaternary amine cations, which in turn adsorb on the negatively charged clay. The adsorption of hexadecyltrimethylammonium (HDTMA) and octadecyltrimethylammonium (ODTMA) on montmorillonite was studied above and below their critical micelle concentrations (CMC). At concentrations above the CMC, the loading exceeded the clay's cation exchange capacity (CEC) and indicated higher affinity of the cation with the longer alkyl chain. An adsorption model could adequately simulate adsorption at concentrations below the CMC, and yield fair predictions for the effect of ionic strength. The model indicated that above the CMC adsorbed micelles contributed significantly to the amount of ODTMA adsorbed. Evidence for adsorption of ODTMA micelles on montmorillonite was provided by X-ray diffraction, freeze-fracture electron microscopy, and dialysis bag measurements. SFM was not adsorbed directly on the clay mineral, and adsorbed at low levels, when the organic cation was adsorbed as monomers. In contrast, a large fraction of SFM adsorbed on the clay mineral when incorporated in micelles that adsorbed on the clay.Peer Reviewe

Vascular thrombus imaging in vivo via near-infrared fluorescent nanodiamond particles bioengineered with the disintegrin bitistatin (Part II).

The aim of this feasibility study was to test the ability of fluorescent nanodiamond particles (F-NDP) covalently conjugated with bitistatin (F-NDP-Bit) to detect vascular blood clots in vivo using extracorporeal near-infrared (NIR) imaging. Specifically, we compared NIR fluorescence properties of F-NDP with N-V (F-ND

Pharmacodynamic studies of fluorescent diamond carriers of doxorubicin in liver cancer cells and colorectal cancer organoids

BACKGROUND: We recently reported on preferential deposition of bare fluorescent diamond particles FDP-NV-700/800nm (FDP-NV) in the liver following intravenous administration to rats. The pharmacokinetics of FDP-NV in that species indicated short residency in the circulation by rapid clearance by the liver. Retention of FDP-NV in the liver was not associated with any pathology. These observations suggested that cancer therapeutics, such as doxorubicin, linked to FDP-NV, could potentially serve for anti-cancer treatment while sparing toxicities of peripheral organs. PURPOSE: To generate proof-of-concept (POC) and detail mechanisms of action of doxorubicin-coated FDP-NV-700/800nm (FDP-DOX) as a prospective chemotherapeutic for metastatic liver cancer. METHODS: FDP-DOX was generated by adsorption chemistry. Experimental design included concentration and time-dependent efficacy studies as compared with naïve (baren) FDP-NV in in vitro liver cancer cells models. Uptake of FDP-NV and FDP-DOX by HepG-2, Hep-3B and hCRC organoids were demonstrated by flow-cytometry and fluorescent microscopy. FDP-DOX pharmacodynamic effects included metabolic as well as cell death biomarkers Annexin V, TUNEL and LDH leakage. DOX desorpted from FDP-DOX was assessed by confocal microscopy and chemical assay of cells fractions. RESULTS: FDP-DOX efficacy was dose- and time-dependent and manifested in both liver cancer cell lines and human CRC organoids. FDP-DOX was rapidly internalized into cancer cells/organoids leading to cancer growth inhibition and apoptosis. FDP-DOX disrupted cell membrane integrity as evident by LDH release and suppressing mitochondrial metabolic pathways (AlamarBlue assay). Access of free DOX to the nuclei was confirmed by direct UV-Visible fluorescent assay and confocal microscopy of DOX fluorescence. CONCLUSION: The rapid uptake and profound cancer inhibition observed using FDP-DOX in clinically relevant cancer models, highlight FDP-DOX promise for cancer chemotherapeutics. We also conclude that the in vitro data justify further investment in in vivo POC studies